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Old 02-20-2017, 06:39 AM   #1
blablabla
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Default Counting RNA-seq data

I have RNA-seq data in terms of aligned reads.
Now I just want to quantify the read counts per bp w/o the consideration of the overlap w/ any feature (example result file [1]). How can I do that?

[1] http://www.ebi.ac.uk/arrayexpress/fi....basecount.txt
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Old 02-20-2017, 10:32 AM   #2
Brian Bushnell
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With the BBMap package:

pileup.sh in=mapped.sam basecov=basecov.txt
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Old 02-21-2017, 12:50 AM   #3
blablabla
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Thank you, exactly what I was looking for!

Quote:
Originally Posted by Brian Bushnell View Post
With the BBMap package:

pileup.sh in=mapped.sam basecov=basecov.txt
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